Paralysed
by IzzieStar
Summary: Sequel to Valentine's Day in Atlantis. John and Elizabeth have been torn apart by the IOA...until John is involved in an accident.
1. Chapter 1

Elizabeth stared out into the ocean with her jaw set in a firm line. From the outside she appeared calm, such as the surface of the ocean which she was staring into, but beneath, her chest was pounding, and if you looked a little closer she was surreptitiously wringing her hands. Behind her, John Sheppard was sat on her (their) bed staring at the wall opposite him. Neither had said a word since her meeting with the IOA. Neither needed to. It was all too obvious to bother using words.

She cursed herself for her stupidity. They had never taken a risk before. Their routine had become as natural to her a breathing. And then one night John had grabbed her in her office and leaned in for a kiss. And there was Steven Caldwell – the disgust on his face quickly followed by a smirk which confirmed all of Elizabeth's fears. He told the IOA. Of course he told the IOA. Not only was he looking for a way to take the leadership of Atlantis, but Elizabeth was pretty sure he still wanted to get even after she'd turned him down.

That was all irrelevant now though – her main task was to try and persuade the IOA that she was still capable of doing her job, and John his. And the small matter of ending their relationship.

'Is there no way...we can, I dunno, persuade them that none of this affects work?' John asked.

'Wolsey made the situation pretty clear – we end this or we're being sent back to Earth.' Elizabeth said sadly.

'No chance of talking him round?'

'No.' Elizabeth said sadly.

She went over to the bed and sat down, taking his hand in her own, hoping to comfort him. It was impossible to look at him though. One glance into those eyes and she was pretty sure her heart would break.

'We could walk.' He suggested lamely.

'I would never make you do that John. I know how much you love this place and your job.'

'I know. I couldn't do that to you either.'

'So we tell them that it was just sex, nothing more and...' Elizabeth paused.

'And?' John asked.

'And we end.'

Quickly, she looked down at her feet, to hide the tears that were beginning to form in her eyes. The pain was raw and her whole heart felt like it was collapsing. Her resolve remained unshaken though – they would do this. Never again would they share this bed, and never again would she sit by his side with their hands entwined. It was for the best, but, God, it was hard.

'We could carry on in secret...'

'No. They'll be watching our every move like hawks, we'd get caught.'

From beside her he got up, and walked over to the other side of the room and promptly kicked her waste bin against the wall. She immediately went over to him and clung to him. After a few seconds he gave in to his emotions and wrapped his arms around her and breathed in that scent of coconut which was so familiar.

'I love you so much.' Elizabeth said hollowly.

'I love you too.' He replied and squeezed her tighter.

They remained in one another's arms until John's watch beeped to tell him that he had a meeting with the IOA which meant he was walking away from all of this for good. With one final kiss, he left her quarters for good.


	2. Chapter 2

**6 months later.**

Since Doctor Ben Hill's arrival Elizabeth had began to feel more like herself again. Losing John had been devastating, truly shaken her to the core, and, subsequently, she had pushed away her friends in a poor attempt to move on and forget him. It turned out that paperwork wasn't a very good replacement for human interaction though, and she was rather grateful for this little friendship she had struck up.

It was almost two years since Elizabeth had requested a historian to plough through the data regarding the Ancients and the Pegasus Galaxy, and two months ago Elizabeth had been one of the most surprised when he request was finally approved and Ben had been sent over.

Initially, she hasn't really had much time to interact with him, but from hearsay and the odd passing on the corridor, she had surmised that he was a nice, if rather quiet guy who kept himself to himself, but had struck up a good friendship with Zelenka. Then he'd asked for her personally to help him with some translations and her opinion of him began to evolve as they became more comfortable in each other's company and the conversation began to flow with ease.

Over the next two months they came to work together again a few more times and over that time she could honestly say that Ben had become her friend, and her respect for him grew greatly. Just before he had been offered the job his fiancée had left him for another man and he had decided to really make something of his life and that's when the offer from the SGC had come in. There was no way he was going to say no. In that respect, Elizabeth envied him and was very conscious of the fact that, in contrast, she had become a shell of her former self and life meant getting through paperwork and moving from one decision to the next.

Ben helped her move on from that. She became aware of that when she joined him and Zelenka for dinner in the mess hall. It was the first time she had eaten a meal in the public eye since she had been with John. Naturally people had assumed that she was romantically involved with Ben (who could blame them after news of her and John had spread through the city like wildfire), but she didn't have time to persuade people that they weren't, and if she did they wouldn't believe her anyway.

Because she really wasn't. Elizabeth was very aware of that as she sat down across from him in the mess hall with her tray and gave her a half smile before returning his attention to the tablet he was looking at. He had assumed the role of a big brother mingled with an old friend, she thought to herself. It wasn't that he was physically unattractive; it was simply that the chemistry wasn't there and it was clear from the outset, that after their past experiences, neither of them wanted a potentially messy relationship.

It bothered John. She knew it did. She saw it on his face every time she sat down with this other man to share dinner with him. She saw that look of confusion and pain, quickly followed by nonchalance and pretence that he was partaking in a conversation. Elizabeth sighed. They never spoke now. Apart from briefings which had become excruciating for her; unable to look and John and his whole team studying their body language for the duration of the meeting. At first they had managed to pass niceties, and then Elizabeth heard that John had slept with a villager on one of his team's missions. The fact that he could barely look at her in the following days seemed to confirm it. If she had been in a rational mindset, she would have accepted that, given that they weren't together anymore, he was allowed to sleep with whoever he wanted. Irrationally though, it felt like a great big betrayal and a slap in the face. It still did.

'You're looking perturbed.' Ben commentated.

Elizabeth came back to her senses, 'Me? Just tired.'

'It's your own fault.' Ben said with a smile.

'I know. I'm your resident workaholic.' Elizabeth said putting her hands up.

'You could take a night off. Radek and I were going to watch a film; you'd be more than welcome to join us.'

'That's kind, but I have memories of Radek's taste in films.' Elizabeth said.

'You choose then.'

'Seriously, I have work.' Elizabeth said.

'Work which will still be there in the morning. Go on...' Ben said.

'You're being very cruel Doctor Hill.' Elizabeth said with a smile.

'And if you don't come, I could always go and tell Carson how tired you are.' Ben said.

'Fine! I'll come.' Elizabeth said.

The last thing Elizabeth needed was Carson on her back about her lack of energy – she had so much work to do, and although she appreciated the concern she couldn't risk taking the day off that she was pretty sure he would demand. And she was pretty sure she could probably sneak back to her office after they'd finished the shortest film she could find.

'Doctor Weir and a medical team to the control room.' A voice in her ear demanded.

Elizabeth stood up feeling confused, with a quick apology to Ben and hastily walked to the control room. The sight she was faced with was distressing to say the least. John's unconscious body lay in Ronon's arms with a constant drip of blood falling to the ground from his head.

'John.' Elizabeth said through a broken voice.


	3. Chapter 3

The world seemed to pass in a blur as she stood rigidly still in shock. Flashes of red, blue and orange bypassed her as the medical team rushed to her second in command. Her second self. Since they had split, she had feared this every time she sent him out on another death-defying mission – losing him and never being able to reaffirm how she felt about him. Every inch of her wanted to reach out and comfort him, but she couldn't. Not him, please not him, Elizabeth prayed, let him live.

From behind her she felt a hand rest on her shoulder, rousing her to her senses. She turned to see Teyla with a look of concern on her face.

'We should debrief now.' Elizabeth said slowly, hardly able to get the words out.

The atmosphere was tense, to say the least – worry and exhaustion etched across each of their faces. They needed to stay strong though to establish exactly what had happened and how to proceed with John.

'So how did this happen?' Elizabeth asked.

Teyla began, 'Our negotiations were going well...and then we started to sense something was wrong, the Penturans were very keen for us to stay when it was clear that our terms were agreed. Colonel Sheppard seemed to sense this and we were making to leave when we were faced with Kolya and his men – '

'Kolya?' Elizabeth interrupted, in shock.

'Yes,' Teyla resumed, 'Dr McKay correctly deduced that the whole agreement had been a trap, so we quickly took out as many men as we could and ran for the gate.'

'We should have known then.' Ronon said through gritted teeth.

'Known what?' Elizabeth asked.

'They didn't chase after us, we just assumed we'd been lucky and carried on back to the gate. Anyway, Sheppard stayed back to do his lace and told us to keep going...Then just as we got to the gate we heard an explosion and when we went to check it out Sheppard had been hit and landed in a pretty awkward position, unconscious...and they were after us again. We managed to make it to the gate and here we are.' Rodney finished solemnly.

'Kolya had tricked you into heading back to the gate.' Elizabeth said.

'It looks that way.' Rodney admitted.

'And John's been out the entire time?' Elizabeth asked.

'Yes.' Rodney confirmed.

Elizabeth nodded, sat back in her chair and ran her hands through her hair. Those bloody laces. Her never bothered to double knot them. On hearing Kolya had been involved her first instinct had been to send a team out to hunt him down and kill him. That wasn't the right thing to do. It sure as hell would have felt good, but she couldn't allow herself to do that. Doing so would have proved that the IOA was right all along – her relationship with John _did _affect her rationality.

'Are you okay?' Teyla asked.

'Me? Fine.' Elizabeth smiled.

'You don't have to lie. We're not the IOA.' Rodney said with uncharacteristic kindness.

'I feel terrible, as I'm sure you do. For now, we just have to put John first and leave our feelings as an afterthought. I needed to go down to the infirmary.' Elizabeth said.

Once away from John's team, Elizabeth found herself a secluded corridor where she could lie against the cool wall and allow the release of the tears which had been threatening to make an appearance since she'd seen him. With a wipe of her sleeve over her face, she felt ready to continue with the face of a diplomat.

The sight she was met with was even more terrifying that the one she had been prepared for. The infirmary was in chaos with medical staff dashing around with surgical equipment and, across the room, John was led on an operating table with Carson standing over him preparing to make an incision. As if sensing her presence, Carson looked over at her and shouted, 'Can somebody brief Doctor Weir, please?'

It was serious then.

A junior Doctor guided her into Carson's office and closed the door. 'He's going to die', was her initial thought.

'Hey. Can I get you a coffee or something.' Dr Harris asked her.

'No thank you.' Elizabeth said politely, all the while thinking, 'just spit out!'

'Okay. Colonel Sheppard has experienced a very traumatic head injury and consequently there is internal bleeding. We are opening him up to assess the damage and stop the bleeding...' Dr Harris said hesitantly.

'But?' Elizabeth asked knowingly.

'But, given the impact there is a chance of brain damage. To what extent we can't be sure yet, but you should be aware that there is a chance.'

'That means there's a chance there isn't though.' Elizabeth said optimistically.

'Of course. He's got the best people in there with him. I'm sure this is very hard for you.' Dr Harris said, squeezing her hand.

Elizabeth immediately retracted her hand defensively, 'And what it that supposed to mean?'

'You two used to date, I just thought...'

'I care about every single person on this mission – seeing any one of them in this position would be upsetting.' Elizabeth said, standing up.

'I'm sorry.' Dr Harris said, looking terrified.

Elizabeth felt a pang of guilt and sat back down, 'I'm the one who should be apologising. I – you're right, this is hard for me.'

'We could give you something – a valium or something.'

'No. I'll be fine. John's going to need every single one of you. Let me know when he's out of surgery. 'Thank you.' Elizabeth said.

Leaving the room, Elizabeth saw John's helpless state and wondered if a valium might have been a good idea. There was no a hope in hell that she was going to be able to concentrate on a single task – never mind sleep. She then felt the urge to go to their balcony.

When she arrived, a small lump formed in her throat. Rarely, did she find herself here these days although this was the place where she felt closest to John, where they'd shared so many memorable moments as friends as well as lovers. After a hard day, they had instinctively known the other would be there and, sometimes, they didn't even need to talk about it. Being with each other was enough. How she had fought her feelings; she had never even dared to let herself believe that she could be John's sort. And then that night, almost a year ago on Valentine's Day she had seen the way he looked at her and the way it felt in his arms and she allowed herself to wonder and look where that had got her.

There had been so many good times, but in hindsight, maybe it would have been easier if she's pushed him away at the start. Too late for what ifs now though, she was here and she was hurting, and he was there and he might not even know her when he woke up.

'Doctor Weir to the infirmary.' Carson's voice beckoned.


	4. Chapter 4

Shakily, Elizabeth made her way into his room and shut the blinds; she needed privacy for this. The bandage on his head made him seem so weak, so fragile – she was almost too scared to go near him for fear of breaking him. Tentatively, she sat on the end of his bed and clutched his hand and stroked it.

'Hi. It's me. Elizabeth. No idea if you can hear me, maybe it's probably better that you can't – I'm tired and I don't really know what I'm saying, but I wanted to be here. With you. No doubt the rumour mill is going into overdrive out there, Doctor Weir all alone with Colonel Sheppard. Anyway, you came through the surgery – of course you did, why else would I be here? Well, you came through it...well. No brain damage – they shaved a bit of your hair off, but I'm sure you'll forgive them.' Elizabeth paused and squeezed his hand, 'I was so scared when I saw you like that in the control room. I guess it brought a few facts home. Not least that you aren't some super hero who can take on anyone, no matter what the odds, and come back unscathed. I always told you to double knot your laces and, being John Sheppard, you never listened. That's not important now though. So, I was saying...seeing you like that it scared me and all I could think was, 'I wish I'd told him how I feel'. So I'm telling you John. I'm telling you how I feel.' Elizabeth took a deep breath, 'It doesn't really stop hurting, does it? When you love somebody so selflessly, so intensely. I can't remember a day when I haven't thought about quitting so we can be together – there's even a resignation letter in my desk. I know you'd never let me go through with it though, and I know that I could never give you that ultimatum – that's why I feel like this in the first place. The resignation letter. I wrote it on the day when I found out about you and that girl. If you were awake, I'm sure you'd deny it, but I know. I know you slept with her. And why shouldn't you? You're an attractive, single man. I know that.' Elizabeth sighed, 'It's just that I'd rather foolishly allowed myself to believe that in not being together we'd still remain loyal to one another. So I wrote that resignation letter all ready to return to earth with the hope that you would die a painful death by Wraith, well maybe not that cruel, but some gentle torture would have been appreciated, and then Ben Hill walked into my office needing help and he provided a welcome diversion – gave me a chance to get my thoughts clear. I'm not in a relationship with him, John. I know you've wondered – I've seen it in your face and maybe I let you believe that to punish you which was wrong of me. He's been a good friend John. Both him and Radek. When we split up, it only seemed fair to let you have our friends – they're your team after all and I don't resent that, I am truly glad that you have a group of such good people to support you. And, part of me was scared of facing them, given that we'd been lying to them for months.' Elizabeth held his limp hand to her cheek and kissed it. 'I love you and I realise you probably still know that, it just feels like a long time since I told you. I wish so much that you would open your eyes and say you love me too, there's even a flicker of hope inside me now that you will, but Carson says you won't be coming round for a few hours yet. When you're wake up, I will be here for you. The IOA can go to hell, because you're going to need me. John, when you wake up, you are probably going to never wish you did. It wasn't just your head that was damaged in the explosion, you spine was damaged and, Carson can explain the ins and outs, your left leg is paralysed. There is an operation, but the chances are slim and Carson wants to make sure you're sure of what you are doing before committing to an operation which could potentially leave your spine even more damaged. Whatever happens though, and whatever you decide, I want you to know that I will be right by your side.'


	5. Chapter 5

The wait was killing her. Her eyes invariably were on the clock and her mind was counting down with the hope that when she got to zero Carson's voice would be there. It had been six hours. Admittedly, Carson had said it could take anything up to twenty-four hours, given the swelling and the general anaesthetic, but he was strong and she'd just assumed...

How was he going to react when he woke up? Even she hadn't quite let the news sink in yet. Paralysed. John. Fucking hell.

She looked up to see Steven Caldwell sauntering over with two coffees. Great. Just what she needed. Since he'd caught her and John she never quite knew how to be around him, unsure of whether he still respected her or thought she was a liar and poor leader. Probably the latter.

'I thought you could do with a coffee.' He said, putting one on the desk and sitting down across from her.

'Thanks.' She said.

'How is he?' Caldwell asked after a pause.

'Still unconscious, but the surgery went well.'

'Good.'

Elizabeth eyes rose to met Caldwell's and, seeing the sincerity, she smiled and nodded. An uncomfortable thought was niggling at her; she _should _tell him about the paralysis, as the most senior military person in the city at this moment in time. Somehow, it felt wrong to tell him though, before John knew. Telling him whilst he was unconscious didn't really count.

'You look tired. You should go to bed.' Caldwell said.

'I should. I'm going to wait for him to come round though.'

Caldwell's eyes narrowed, 'You two aren't...?'

'Of course not! You don't honestly think I'd be that stupid?'

'History suggests so.' He said with raised eyebrows.

'I guess I deserve that.' Elizabeth said looking down into her coffee.

For some inexplicable reason, she still felt guilty about the way she had treated Caldwell. It wasn't as if she had led him on in any way, or ever indicated that she interested in him, and yet she still felt the need to apologise every time she saw him. Maybe it was that look of disappointment that still lingered in his eyes. That look that said, 'with him, as well'. Even without John, she would never have dated Caldwell – he wasn't her type, too serious, too uptight...

'No you don't. You've had a tough day. I just thought I'd bring you a coffee and if you need to talk, I'm here.' He said.

Wow. Where had that come from?

'Than- '

'Dr Weir report to the infirmary.'

Elizabeth quickly stood up from her seat in a motion that tipped it over and strode out of her office, leaving the fallen chair and Caldwell behind. He was awake. Inside her chest her heart was pounding with relief mingled with nerves and fear. Even with the assistance of a transporter, the journey seemed to take twice as long as it usually took. Carson was already stood outside waiting for her.

'What's wrong? Is John okay?'

'He's fine...just a wee bit fragile at the moment. He knew immediately.' Carson said with a regretting look in his eyes.

'Did you explain about the procedure?'

'I have, but he knows the risks and I've given him some time to think about it.'

'Is he up to seeing me?'

'Aye. Go on in, I'm off to get some rest.'

Slowly, Elizabeth pushed the door open and shyly looked over at the side ward. The blinds were closed. She smiled to herself. John would hate the idea of people seeing him bandaged and weakened. When she entered the room he managed to force a smile, but it didn't meet his eyes. Returning it, Elizabeth sat down next to the bed.

'Didn't expect to see you.' He said hoarsely.

'I'm your boss, John.'

'S'that all?'

Ignoring his comment, she said, 'How are you feeling?'

'Like I wish I hadn't got out of bed this morning, or yesterday morning or whenever it was.'

'I'm so sorry.'

'Yeah, me too. Kinda grown fond of walking.'

Elizabeth sighed. If the only way he could deal with this was sarcasm, then she was fine with it, but in some ways it would have been easier if he'd broken down and cried. At least she would have known how to comfort him.

'So why are you here?' He asked.

A hint of annoyance hit Elizabeth and then faded immediately.

'I wanted to check that you were okay.'

'Well, I'm fine. You can go to bed now.'

'Is that what you want?'

'It beats sitting here wasting oxygen trying to ignore everything that's happened over the last six months because I'm now an invalid.'

'From memory precisely nothing has happened in the last six months. Aside from you shagging that Nerisan.' Elizabeth shot coolly, piercing him with those cool eyes.

'Really? How is Ben?' John hit back, even cooler.

Elizabeth couldn't help but let a smile escape from her lips. He thought she was being cruel. In fact, she was being quite the opposite. Languishing in his suffering would only wind up driving him mad. Challenging him, giving him something to get his teeth into would reignite that fighting spirit. And he was going to need to be a fighter.

'Just fine. Well he was when I saw him at dinner.'

'Good. Send my regards.'

Elizabeth stood up and walked over to the door, resting her hand on the handle before turning back to him.

'I thought you knew me better John Sheppard.'

'And what's that supposed to mean?'

'I'm not dating Ben, not sleeping with Ben. We're just friends.'

When it came down to it, she couldn't let him believe that anything was going on between her and Ben. That would have been too malicious. Even if it was all in the name of a good cause.

'I didn't think you were.' John said gently, meeting her eyes.

Pulling down on the handle, Elizabeth nodded before leaving the room and closing the door behind her. Hearing it click she let out a deep breath.

A/N: Little bit unconfident about this fic. Would love to hear some reviews.


	6. Chapter 6

After thirty seven hours and approximately twelve minutes of being awake, Elizabeth Weir had finally found her bed and fallen asleep almost instantaneously. It hadn't been an uninterrupted sleep though, unfortunately. Images of John with blood dripping from his head were trespassing on her dreams and, after five hours, Elizabeth gave up and dressed again.

Bleary eyed, she made her way to the mess hall to grab some coffee. As soon as she entered the hall she was approached by about twenty or so people asking after John. Most of which, she was amused to see, were young women with wide eyed concern. Trying to appear as professional as possible, she told them that he was 'making good progress', as she was pretty certain he wouldn't want her revealing the extent of his injury to everybody just yet. That reminded her...she needed to tell Caldwell. After a quick mental debate, she decided it could wait for a couple of hours. She really didn't fancy the idea of him buzzing around her all afternoon suggesting changes to training routines or the teams that were in place.

After grabbing a bagel, Elizabeth headed over to her office where she could lose herself in the monotony of mission reports and indulge in the secret supply of Hershey's which were tucked safely away in her desk. Biting into the first bar Elizabeth gave a small sigh of pleasure and looked up to see an uncomfortable Carson at her doorway.

'Oh, Carson, excuse me. Come in.' She said through a mouth of chocolate.

'It's just a flying visit. I was wondering if you could try and drop into the infirmary today and see John.' Carson said with a hopeful smile.

'Err, sure. Why?'

Carson looked slightly puzzled at this question, 'I thought it might cheer him up a bit. And he's refusing to see anybody else.'

'Of course. You know what? This lot really can wait.'

Technically, that had been a lie and she knew the pile would be even bigger when she got back, but John came first. Deep down, there was a feeling of reluctance about seeing him again. Spending more time together meant they'd be running out of small talk and would eventually start talking about their feelings which was dangerous territory. How could she say no to a man who was suffering so much already? That was if he still wanted her. She wasn't so sure now; the bitterness with which he faced her during their last meeting was shocking. A part of her had always hoped...Stop it, she told herself.

The room was dark when she entered it, and she paused to hear his breathing before turning it on. It was too rapid for him to be asleep so she slid her hand over the panel. His eyes were wide open staring into space and her heart suffered a jolt to see him so dejected.

'Another duty call?' He asked without looking at her.

'I brought you a Hershey's.' She said, offering the bar.

'Great. Just what I needed.'

The bar remained in her hand and she delicately placed it on the surface next to him before sitting down.

'I could get 'War and Peace'.' She offered.

'Don't. You're spoiling me.' His tone was lifeless.

'We could have sex.' Elizabeth suggested coyly.

That got him. He sat up slightly and looked at her for the first time. In reply, Elizabeth smiled sweetly and tapped her fingers against the chair.

'What do you want?'

'Nothing. I'm here for you, anything I can I do for you, I will.'

A small smile played around his lips, 'I quite like the sex suggestion.'

That's better, Elizabeth thought to herself. With her (minimal) rejuvenation from sleep, she was even more determined to make sure he didn't fall into despair, even if that meant sitting by his bedside all day. Well, maybe not all day. Caldwell might start trying to hunt her down and run to the IOA again, reporting occurrences of more than five minutes spent in one another's company.

'Have you told anybody yet?'

'It's not my place John. I am going to have to inform Steven Caldwell soon though.'

'He'll be taking my job.' John said with realisation.

'Temporarily.'

He gave her a pointed look.

'Have you thought about the operation at all?' Elizabeth asked tentatively.

'Haven't stopped.'

'And?'

'And I'm still thinking.'

Elizabeth smiled, 'You sound like Ronon.'

John laughed slightly, 'Sorry.'

'Don't be. I can't even begin to imagine what you are going through.'

'Of all the things that could have happened...I think I'd rather be dead that stuck like this for the rest of my life.' He said bitterly.

With a sudden motion she moved onto his bed, aching to comfort him. Gently she took his hands in her own and traced circles on his palms with her thumb. Words would do nothing to ease the pain he was suffering. _Nothing _would ease the pain he was suffering. But she had to be there for him somehow.

'You probably have work to do...' He said.

'It doesn't matter.'

'Liar.' He said.

'Well. It doesn't matter as much as you do.'

'Nevertheless, I know you'll probably end up spending half the night catching up if you don't go and I should get the rest.'

'I can stay...'

'Go.'

As means of goodbye, she leant out to stroke his cheek and she stood up to leave, but he caught her by the wrist and pulled her back. Unsteadily she met his eyes and saw her own desires and longing reflected in his.

'Don't.' She pleaded.

Ignoring her, he ran his hands through her hair and pulled her into his body enveloping her in his body. She was powerless. With one defeated groan she pressed her lips into his, kissing him passionately, reaching out for every inch of his body trying to reclaim the time they had lost.

And then she stopped.

'I can't...it's taking advantage.' Elizabeth said stepping away from him.

'Get out.'

'I-'

'JUST GET OUT!' He roared.

Tears spilling from her eyes, she fumbled for the door and ran.


	7. Chapter 7

Finding the nearest bathroom, Elizabeth locked herself in and splashed her flushed face with water. Seeing her reflection in the mirror, she groaned and sat back on the toilet seat. She looked terrible. At least she'd stopped crying. He'd been _so _angry. It had scared her if she was honest. Never, had he shouted at her; raised his voice, sure, but this was different. The emotion in his voice was raw and distraught.

Feeling his kiss had been a...relief. It was the only way she could describe it. For that couple of seconds she had let herself go and remind herself of what he was to her. It couldn't happen again though. They were too confused at the moment; too many conflicting emotions dictating their actions. And, they still worked for the SGC and the IOA. She hadn't even thought about telling them about John's injury yet. They had a dial-in scheduled for the following day and, if it was okay with John, she would tell them then.

And then there was Caldwell. She _had _to tell him this afternoon. Working beside him everyday wasn't the most desirable relationship in the world, but he was the most qualified and the SGC would back him until John returned. If John returned.

There was a twenty-seven per cent chance that the surgery would be a success – and that was if he decided to go for it. Instinctively, she knew he would. He wouldn't give up. There were so many things that could wrong though and, if they did, he would be returning to earth. Permanently. It didn't bare thinking about.

Could she really let him go? Once again she would have to choose between the man she loved and her whole livelihood and this time she wasn't so sure the latter would win. When she had seen him immediately after the surgery she had told him that she would be right by his side, and she was going to stick to that.

Feeling more certain of herself, Elizabeth reached for her radio and said, 'Colonel Caldwell, report to my office. Weir out.'

By the time Caldwell arrived in her office, she was sat with her usually poise behind her desk and gestured for him to sit down with a smile on her face which didn't betray her inner turmoil.

'What can I do for you?' Caldwell asked.

'How would you feel about taking command of the Military Contingent of Atlantis, temporarily?' Elizabeth asked.

'Until Colonel Sheppard returns?' Caldwell asked.

Elizabeth sighed, 'Unfortunately, apart from the injury John sustained to his head, there was an injury to the spine. I'm afraid John is now paralysed in one leg. Doctor Beckett has informed me that there is an operation which could potentially correct the damage, but it is incredibly complicated surgery with numerous risks involved and no guarantee of success.'

'And you have only just decided to tell me this?' Caldwell asked, narrowing his eyes.

'Excuse me?'

'I should have been informed as soon as you were.'

'I have a duty to the people of this city, and I chose to respect Colonel Sheppard's privacy until I could speak to him.'

'I appreciate that, but it's interesting how you seem to feel so much more duty to him than the rest of the city Elizabeth.'

'I really don't have time for this, Steven. Are you willing to take on the role or not? I'm sure Major Lorne would be willing to step in.'

'I'll take the job. When are you informing the SGC?'

'At our scheduled dial-in tomorrow. For now, I'd prefer it if you kept the news to yourself. That will be all thank you.' Elizabeth said curtly.

Looking mildly irritated, Caldwell left the office. The meeting between them had only confirmed Elizabeth's fear that working with him alongside her, questioning her decisions, proposing his own strategies...She groaned. Beyond their less-than-platonic relationship, Elizabeth trusted and respected John on every level as a colleague. With Caldwell, she simply didn't have that. It was going to take some time to get used to him. And even then, she wasn't sure she would she would be completely comfortable with him.

Overlooking the control room, Elizabeth became very aware that Rodney was making a bee-line for her direction and sat up slightly to hide her foul mood. He marched into the room and closed the door behind him. The look on his face suggested he was in a confrontational mood.

'What's going on with Sheppard?'

'He's still in the infirmary.' Elizabeth pointed out, trying to buy time.

'I know that. Why isn't he seeing anybody?'

'He's just had surgery Rodney, I'm sure Carson has him under strict orders to get plenty of rest.'

Hearing this, Rodney seemed to relax a little, and Elizabeth gave a sigh of relief, inwardly.

'So maybe this evening?' Rodney said eagerly.

'Maybe. I haven't really had the chance to talk to him or Carson yet. As a precaution though, I've installed Colonel Caldwell as the acting military leader of Atlantis.'

'John's okay with that? I mean I'm not Caldwell's biggest fan, but John hates him, especially after he -' Rodney stopped dead in his tracks with realisation, 'I, err, should probably get back to my lab.'

Elizabeth tried to suppress a smile, 'Probably.'

Blushing slightly, Rodney nodded to Elizabeth and left. Finally. Some peace.


	8. Chapter 8

After sneaking a power nap (a much needed power nap), Elizabeth went for dinner, desperately hoping that Ben would turn up. It was half past six and they had generally fallen into a routine where, barring a catastrophe, they would meet at this time to catch up, or simply eat share a meal. By the time Elizabeth was eating her fruit salad, she was giving up hope, and then he strolled in scanning the room for her, smiling and waving when he saw her.

As soon as he sat down with his dinner, he asked, 'How is he?'

'He's paralysed.' Elizabeth revealed, in a quiet voice.

'What?' Ben asked, in shock.

'There was damage to his spine and he has no feeling in his left leg.'

'Shit. He must be devastated.'

'He is. I've never seen him like this; it's like his completely given up hope, he won't see anybody not even his team, and with me it's so messy, almost like he doesn't know how to behave.' Elizabeth confessed.

'He's just a really traumatic shock, maybe you just need to be a little selfless and put up with that.'

'We kissed. No, before you ask. I stopped it and then he got angry at me. Was I wrong to do that?'

'No, of course not. The last thing he needs is more confusion.'

'That's what I thought. I don't know how to be there for him. Carson says there's an operation, which gives him some slim hope, but what can I say to make it better?'

'Probably nothing, I'm afraid. You should be there for him though.'

Somehow, with his level-head, Ben made it all seem so simple and gave Elizabeth the confidence to make an attempt to visit John. It didn't matter that he might be awkward to around, right now. What mattered was that she was there for him in whatever proximity he needed her to be – well, to an extent.

Carson looked rather pleased to see her when she turned up in the infirmary at nine o'clock. She had spent the past two hours working through papers meticulously to allow herself more than five minutes with him.

'He's just woken up. He's been in a terrible mood all afternoon; he'll be pleased to see you.' Carson said, guiding her over to the side room.

'I'm not sure about that.' Elizabeth muttered.

Pat her lightly on the shoulder, Carson nudged her into the room and closed the door behind her.

'Hey.' She whispered.

'Hey.' John replied.

She remained rooted to the same spot, unsure of how close he wanted her – whether he wanted her there at all – after what had happened. Each time she had seen him, he had gradually looked worse. A grey-tinged paleness had replaced that light tan she was used to and his eyes were sunken like he hadn't slept for days.

'Umm, I wanted to say sorry for this morning.' Elizabeth said.

'I should be apologising. It was wrong to shout at you, and make you cry. I hate it when you cry.' He said.

'And I hate seeing you like this.' Elizabeth said, venturing slightly closer.

'Have you spoken to Caldwell?'

'Yes. He was his usually charming self. Laid into me for not telling him sooner.'

'He didn't send his regards? I'm hurt.' John smirked.

That smirk. The unique combination of raw sex appeal and confidence made her heart flutter even now. Finally, she felt confident enough to relax into the chair.

'That's better. You were making the place look untidy.'

'Apologies.' Elizabeth smiled.

'I've told Carson I'm going to have the operation.'

Elizabeth sat up slightly, 'John, that's really good news.'

'We'll see about that. I could end up losing use of the other leg as well.'

'Do you have any idea when?'

'We need to wait for my stitches to heal yet, so about three weeks or so, and then, if the operation is a success, there'll be physio and stuff so I could be out of commission for up to six months. Six months of working with Caldwell, Elizabeth, it's you we should be feeling sorry for here.' John said, with a teasing smile.

'Five minutes this afternoon was bad enough...' Elizabeth chuckled.

'You never know, you might even grow to like him.'

'I can't imagine working with anybody other than you.'

'I'll take that as a compliment.'

'It is one. I'm informing the SGC tomorrow, is that okay?'

'Sure. Do you think they'll send me back to earth?'

'They have every trust in Carson...'

'If the surgery doesn't work?'

'Your skills would be greatly valued here in an advisory role.'

John smiled, 'That's a yes then.'

'I've taken the IOA on before and I will do it again.'

'You're not at you most credible with the IOA when it comes to me.' John pointed out.

'Nevertheless, you're an asset to this team and the IOA know that.'

John studied her face, with wondering eyes which seemed to read every little thought she had ever had. What he found seemingly pleased him though as he smiled slightly and continued to enjoy looking at her. With any other man, she would have felt uncomfortable and looked away, but John could make such an act seem gentle rather than overly intense.

'You're staring.' Elizabeth pointed out gently.

'And you wouldn't know that I was staring if you weren't staring back.'

'Touché.'

The door opened behind them and Carson's head appeared. 'Five more minutes, you need an early night John,' he said before disappearing again.

'Will you come and visit me in the morning again?' He asked hopefully.

'I will, but if you need some company, I know three people who are desperate to see you.'

John shifted uncomfortably, 'I don't want them to pity me.'

'They won't; they know and love you too much for that.'

'I'll ask Carson to send for them in the morning.'

'Good.'

'But you'll still come and visit me?'

Elizabeth laughed, 'I'll see you in the morning.'

A/N: Thank you very much for the reviews.


	9. Chapter 9

Since waking up at six, Elizabeth had spent the day in a state of nervousness. The dial-in to earth was scheduled for one o'clock and there was no way of telling how Landry was going to take the news about John, and whether she would be accused of inappropriate feelings in trying to persuade them to let him remain in Atlantis. It wasn't as if the appointment of Caldwell had buttered him up enough to fight in John's corner either. So she was on her own.

When she'd visited John, they'd shared breakfast together, and he seemed rather optimistic about the operation and was even looking forward to seeing McKay. She hadn't been able to spend too long with him though as she had to brief Lorne's team on a mission that John's team was supposed to be undertaking. This reminded her that she really needed to reassign Rodney, Teyla and Ronon. She doubted that they'd be too appreciative of having to wait around to see what happened with John before being able to continue with their lives.

After checking stock lists and personal requests for the dial-in, Elizabeth decided to escape and take five minutes on the balcony to get some fresh air with a sandwich which Ben had kindly delivered to her desk. It was spitting, but she didn't really mind. It was just a nice relief to get away from her office.

As she finished off the remains of her rather dry sandwich the door opened and she was joined by a downbeat Rodney. As he got closer to her, he opened his arms for a hug to her surprise. She had never really considered that Rodney could be in need of comfort before – never mind that he would come to her.

'He looks so pathetic.' Rodney said, pulling away.

'I know. You can't let him see you like this.' Elizabeth said protectively.

'Why do you think I'm here? I asked you yesterday – you lied to me.'

'And I'm very sorry for having to do that – it wasn't my place until John was ready for you to know.' Elizabeth said apologetically.

'Why didn't he come to me?'

'I think he was...is ashamed. I know it sounds ridiculous, but John has spent his life being the strong one, protecting everyone else. He hates being the one that needs protecting.'

'He told us about the operation. I think he's mad – risking what he's got left.'

'It'll be worth it if he gets what he's lost back.'

'Which, given the number of potential problems they could run into with that sort of surgery, isn't likely.'

'It's his call Rodney. How are Teyla and Ronon?'

'Teyla was great with him, Ronon less so. He's not exactly brilliant with words at the best of times.'

They exchanged a look and smiled. Elizabeth checked her watch.

'I'm going to have to go Rodney. I have the scheduled dial-in with the SGC. Not sure how I'm going to break the news.'

Elizabeth stared into the waves momentarily, before wondering back into the control room and asking Chuck to dial the gate. She then went up to her desk to wait for the video link. General Landry's face appeared on her screen.

'Doctor Weir, it's good to see you. How are things in Atlantis?'

'We're good, although I do, unfortunately, have some bad news to relay to you. Colonel Sheppard was injured during a mission and is now paralysed in one leg. The good news is that Doctor Beckett is willing to perform an operation which could correct the Colonel's spine. The bad news is that the chances of success aren't particularly high.'

'Surely the best way to proceed would be to return Colonel Sheppard to earth using, the Intergalactic Gate Bridge, where he can receive specialist treatment.'

'Given that Colonel Sheppard has already undergone extensive surgery, I believe that, for now, he should remain here in Atlantis. In his absence, I have installed Colonel Caldwell as acting military leader. I hope that is okay.'

'As the most senior officer there, I see no problem with it. However, given that the Daedalus is scheduled to return to earth next week, you might want to arrange for the Colonel to appoint an acting commander.'

'Will do. I've uploaded our orders for supplies, some of which I'd like to discuss with you, if possible.'

'Go ahead.'

'Firstly, I would like to recruit another translator to the team, specialising in Ancient. Since Doctor Ben Hill's appointment we have discovered vast archives to study and simply not enough people to get through them.'

'I think that can be arranged.'

'And secondly, we are -'

'If you could excuse me for a minute.' Landry disappeared from the screen.

Elizabeth pulled a puzzled face at the screen. That had never happened before. They couldn't be under attack because the gate was already in operation. After five minutes had passed Elizabeth began to wonder whether he was coming back when he resumed his seat.

'My apologies Doctor Weir. One of our IOA counterparts was in the proximity and after hearing our conversation has decided that they wish to conduct a review of the Atlantis expedition, primarily concerning the military contingent in light of Colonel Sheppard's injury. I couldn't dissuade him, but I have bought you two weeks. We'll make arrangements at our next dial-in. Now was there something else?'

Elizabeth was gobsmacked, 'Nothing of importance. It's all in the uploads.'

The wormhole closed and Elizabeth was left with her mouth hanging slightly open in shock. Great.


	10. Chapter 10

At quarter to midnight, Elizabeth was still in her office chewing on her pen and staring into space. Dinner had been forgotten and, below her, the control room was minimally staffed. She looked at the piece of paper in front of her and sighed.

Don't let McKay start any new experiments.

Persuade Caldwell that they should send as few teams as possible through the gate until the review is over.

There was so much that the IOA could find fault with, yet this was all she could come up with as a plan of action. If John had still been her second in command she would have been sat sharing this with him. Caldwell was a different story though; she was torn between the obvious pleasure he took in his new job and the possibility that he might be after her job. Could she risk inviting him to join her little plan of action? Or would he accuse her of trying to distort the facts? _Was_ she trying to distort the facts? Maybe. She just wanted to make sure that the IOA saw the city operating well, and not on the verge of a disaster, so they could fill in their little forms and leave the city in peace.

An instant message appeared on her lap top; 'You promised to visit again today. Only thirteen minutes left...'

Crap. She _had_ promised to visit John again before the day was out and in the midst of worrying about the IOA she had completely forgotten. Her fingers typed 'ten minutes' into the keyboard and she semi-jogged to a transporter to try and fulfil her promise and not be late. As she got to the infirmary she checked her watch. Three minutes. She peeped round into the infirmary to check that she couldn't be seen then scuttled into John's room, hoping she wouldn't be caught. The medical team were the only people in the city, bar John, that could order her around.

'Just in time.' He said.

'I'm so sorry. The IOA have decided to come and review us so I've been a little preoccupied.' Elizabeth apologised.

'It's fine. You're here now.'

Elizabeth reached out for a box of chocolates on the bedside table and took one that looked like it didn't contain a nut.

'These are good.' She said in surprise.

'Yeah. Jessica, one of the nurses, thought they might cheer me up.'

Elizabeth raised an eyebrow, 'I'll bet she did.'

'Is that a hint of jealousy?' John asked mischievously.

Elizabeth threw a chocolate at him which he caught, mid-air, and ate happily. 'So how come the IOA are gracing us with their charming presence?'

'Because of your injury. They want to review the military contingent, although I don't put it past them to be keeping an eye on me as well.'

'You'll be fine.'

'If I can get Caldwell on side. Part of me expects him to undermine me and get the IOA on side.'

'Then you'll just have to make sure he doesn't.'

'And how am I supposed to do that?' Elizabeth asked.

John gave her a pointed look, 'I'm sure you have the necessary tools at your disposal...'

'Wha-? No. No way. No.' Elizabeth said, completely aghast.

'I didn't mean that – just a little harmless flirting.'

'I can't do that.'

'Sure you can. You'll have him eating out of your hand.'

'I'm in a position of authority here – I can't go round manipulating people!'

'Fine. But if you want to keep that position of authority, you might want to give my little idea some thought.'

As Steven Caldwell strolled into Elizabeth's office, Elizabeth began to wonder whether the plan John had cooked up for her was really a good idea. She had approximately two seconds to decide before Caldwell would be sat down in the chair that had so often been occupied by John.

'Good morning Elizabeth.' He said.

'Good morning Steven. I wanted to let you know that in two weeks time we'll be hosts to the IOA for a review. Given your impromptu employment to the Atlantis expedition they decided that they wanted to perform a review. I'm sorry, but the decision was out of my hands.'

'Well that's absolutely fine by me.'

Flirting it is then, Elizabeth thought to herself.

'I'm just glad that I'll be going through this with you by my side.' Too heavy, she cursed herself.

Caldwell sat up slightly, 'Oh?'

Or maybe not. 'You know what I mean. We may have had our ups and downs, but I know you are going to be a fantastic addition to the Atlantis team and I must admit, I'm looking forward to the new dynamics you will bring.'

'I have every confidence that we're going to make a fantastic team Elizabeth.'

Elizabeth cringed slightly, but maintained the fake smile on her face. 'General Landry had a personal request for you. With the Daedalus returning to earth in a week, he would like you to appoint your acting replacement.'

'I'll be on it immediately. But first, do you want to go and get some lunch?'

'I'd love to.'

Okay, she was feeling incredibly guilty about manipulating Caldwell's feelings once again, but...it seemed to be working.


	11. Chapter 11

Elizabeth stood in the jumper bay with Steven Caldwell by her side waiting for Richard Woolsey to leave the jumper so they could meet pass formalities and show him to his temporary quarters. From beside her, Caldwell put his hand on her shoulder and gave her a supportive smile. This really had to stop. Now. Whilst she had appreciated the support that Caldwell had given her in preparing for the visit, primarily as a result of her flirting, he was clearly starting to get a little bit caught up in it all. She knew it was a bad idea when she's decided to go along with it and that it was probably going to end up in a big, emotional mess. As a diplomat she had soon realised that she had to use every route available to broker a deal, but this was taking it a little too far. It was all John Sheppard's fault. John Sheppard was a _very _persuasive man. Too persuasive. She had recently taken to visiting him three times a day, even though she really didn't have the time and she was pretty sure she was falling even more in love with him, which she hadn't thought was possible.

Anyway. Caldwell. In the past two weeks, despite her manipulation which she was deeply ashamed of, she had come to quite like him. Beneath the cold exterior he was actually rather lonely and she suspected that his attraction to her was borne out of this.

Woolsey came into view clutching a small hold-all and numerous suit bags which he was struggling to manage. Fumbling slightly, he stuck out his hand to both Elizabeth and Steven and then asked to be shown to his quarters.

After he had settled into his quarters, he devised a meeting with Elizabeth and arrived with a suitcase from which he withdrew numerous forms and a clipboard.

'I thought we should have an informal interview, clear the air, before the review commences.' Woolsey said sitting down.

Elizabeth raised her eyebrows slightly and sat down. 'What would you like to know?'

'Firstly, I wanted to ask about your opinion on Colonel Caldwell's performance. How are you finding working with him?'

'Surely that is irrelevant.' Elizabeth pointed out.

'I'd just like to know.'

'Steven is a moral person who is willing to listen to other people's opinion and from that devises the best course of action. I am fine working with him.'

'Just 'fine'?'

'Yes. I haven't really had much time to judge his position yet.'

Hearing this, Woolsey scribbled down a note on his clipboard and cleaned his glasses. Elizabeth wondered how he could be so calm and relaxed when he was essentially interrogating her.

'Do you think that you made the right call appointing him as the military commander of this expedition?'

'_Acting _military commander. Given the seniority of his rank, I do.'

'But apart from that, you wouldn't have appointed him?'

'Colonel Caldwell is the most experienced person for the job which, in my opinion, makes him the most suitable personal for the job.' Elizabeth said, beginning to feel slightly frustrated at was turning out to a cross-examination.

Another scribble on the clipboard.

'And how is Colonel Sheppard's recovery?'

'He's doing well. Doctor Beckett is looking to perform the surgery in three days time.'

'It must have been upsetting for you.'

'I'm upset to see anybody on this team hurt.'

Wow. She really hadn't expected 'clearing the air' to be this intense. If the next five days were going to be like this, she was probably going to be an insomniac at the end of the process.

'But you and Colonel Sheppard have developed quite a bond in your time here.'

'If you are trying to imply that, given our former relationship, that my feelings for Colonel Sheppard are beyond that of a colleague, then you are mistaken.' Elizabeth said smoothly.

'Of course not.' Woolsey said. 'You said that Colonel Sheppard is planning to have the surgery in Atlantis, has he not considered returning to earth where he can be treated by specialists and given the time to recover in a more comfortable environment?'

'You'll have to talk to Colonel Sheppard about that.'

'I intend to Doctor Weir. Now, I think that's enough.' Woolsey said suddenly and stood up. 'Good evening Doctor Weir.'

'Good evening.'

After Woolsey had left the office, and Elizabeth felt she could drop the smile, she spun her chair around so the people in the control room couldn't see her and put her face in her face in her hands. The way her had spoken to her... it was almost as if he had decided upon her feelings towards her colleagues and was leading her down a route of questioning which intentionally supported his conclusions. If she got through these five days with her job intact, she was possibly the luckiest woman in the Pegasus Galaxy.


	12. Chapter 12

Elizabeth woke up and dressed feeling incredibly apprehensive about the day ahead. At twelve o'clock John was going into surgery and at five o'clock Richard Woolsey was interviewing her yet again. It hadn't escaped her notice that, in the past three days, he had spent only thirty minutes with Colonel Caldwell and more like three hours with her, questioning decisions that were most certainly not related to the military contingent.

Nobody in the city was beyond the scope of 'the clipboard' as he had been nicknamed, and she had been confronted by some very angry members of the team; Ronon, being one of the most memorable. When Woolsey had suggested that he might like 'to clean up his appearance' because he gave off an 'animal aura', he had found himself with Ronon's gun pointing at him and was backed against the wall when Elizabeth was informed and went to resolve the situation. When she had asked, 'Ronon, what do you think you are doing?', he had replied, 'It's set to stun,' as if that explained the situation and she couldn't suppress the small snort of laughter which hadn't been left unnoticed by Woolsey.

Rodney was also becoming increasingly irritable; unable to start any new experiments and still not able to go off world because Caldwell hadn't found him, Teyla and Ronon a new team yet, he was stalking around the city demeaning the other scientists and taking every available opportunity to remind people how intelligent he was, seemingly worried that they would forget if there wasn't a disaster that he could save them from.

Every evening she went to John and relayed these stories and it was infuriating to see that the incidents that caused her the most stress were the most amusing for him. It was good to see him laughing though. He wasn't laughing today though. As soon as she walked into the side ward, she could see how nervous he was.

'Morning. How are you feeling?' She asked, sitting on the side of his bed.

'Terrified. I think it's only just hit me how much I'm risking here.'

'Are you sure you still want to go through with it?'

'What choice do I have?' He asked honestly.

'You don't have to prove anything to anybody.'

'I know. I just don't want to spend the rest of my life stuck like this, wondering what could have been.'

'That's fair enough.'

'Prepared for your latest inquisition?'

'Hardly. I've generally caught on to the pattern of his questioning now – ask about one of the changes Caldwell is implementing, ask about how you did it, imply that I preferred the way you did it because I fancy you, move onto my decisions, imply that I made a decision because I fancy you, well, you get the gist.' Elizabeth smiled.

'Only two more days left.'

'At the end of which, I may not have a job.' Elizabeth pointed out.

'Well, if this operation doesn't work, at least we'll be getting chucked out together.'

'John, I've spoken to Steven and he really would accommodate you continuing to work as a military advisor.'

'And then the IOA would imply that you made that decision because you fancy me...you get the gist.'

Elizabeth laughed ruefully, 'We will sort something out.'

'I really appreciate that 'Lizabeth, but we both know that if this operation doesn't work I'll be taking the next flight home.'

Elizabeth looked away guiltily. It had already crossed her mind more than once that the IOA would overrule her and Caldwell in such as situation and insist on John returning home anyway.

'Don't worry about it.' John said comfortingly.

'I do worry about it though. I can't imagine the not seeing you every day.'

'It's not like we've really been on talking terms since we split up – you'll barely miss me.'

'That isn't fair.'

'I'm just trying to make it easier.'

'I didn't talk to you because I didn't know what to say. I didn't know how to go from everything we had being friends.'

'And I slept with that girl.'

Elizabeth felt as though her heart had dropped slightly. She could believe that there was a chance he hadn't if he didn't say it out loud. And he'd ruined that.

'We don't need to talk about that.' She said.

'I slept with her because I was hurting. I thought it would make it easier.'

'And did it?'

'No.'

'Not much does.'

'I love you; you know that, don't you?' He asked.

Elizabeth nodded, 'I love you too.'

Slowly, she manoeuvred her body so she could lie beside him and he cuddled her into his body kissing her head lightly. This really was risky and, if they got caught, both of them could well be sacked, but they needed to share this. Make some attempt to heal the painful feelings and comfort one another.

'We're both screwed if somebody walks in right now.' He said.

'I was just thinking the same thing myself.'

'I don't see you moving.'

'Maybe I'm fed up of pretending.'

'What are you saying?'

Elizabeth sat up again and looked into his eyes, 'I don't know.'

'You're just saying this because - '

The door slid open and Carson walked into the room with his notes. 'I'm afraid I'm going to have to ask you to leave Elizabeth, we need to get him prepped for surgery.'

'Can I just have two more minutes?'

Carson nodded kindly and shut the door behind him.

John resumed his speech, 'You're confused because I'm like this.'

'I'm saying this because I love you.'

'We'll talk after the operation. We're not committing to anything now.'

Elizabeth nodded and hugged him, whispering in his ear 'good luck', as she did so. As she pulled away she kissed him gently on the lips and then stood up and left.


	13. Chapter 13

Since one o'clock her concentration had gone out of the window. She had intended to spend the afternoon preparing for the meeting with Woolsey, instead she had invariably been staring at the clock, checking her radio to make sure she was contactable and 'passing' the infirmary so she could pop her head in and check everything was going okay. So far, everything was, and it meant that John was another step closer to coming out of theatre unscathed. The same couldn't be said for her interview.

From what she had gathered, this was to be her last meeting with Woolsey before he tied up a few loose ends and wrote up his report to return to the IOA with. What she wouldn't give to have a sneaky glimpse at that report...there was no point even considering it though; Woolsey was way too straight laced.

When she arrived at her office, she was shocked to see Woolsey already waiting for her, looking at her book collection. She had given herself ten minutes time to relax and have a coffee, but that had just gone out of the window. She sat down behind her desk and Woolsey leisurely strolled across the office to sit down. With his clipboard.

'You have a lot of books Doctor Weir.' He commented.

'That's only about half of them – the rest are in my quarters.' She shrugged.

Woolsey smiled and looked down at his clipboard. 'I take it Colonel Sheppard's surgery is going well?'

'Yes.'

'Good. Let's get started. I was looking over the various trade agreements you have with different partners, how often are these agreements reviewed?'

'Annually. However, if our trading partners meet times of hardship, or we are lacking in supplies then the reviews occur sooner.'

'You have several trading agreements with the Athosians, how instrumental was,' Woolsey looked down at his papers, 'Teyla Emmagan in securing these agreements.'

'She was very helpful in setting up communications between us.'

'So, she was pushing for these agreements?'

'I didn't say that, Mr Woolsey. When it became clear that both parties had something to offer, she helped in the process of securing the agreement. Nothing more.'

'Okay. And Miss Emmagan's relationship with Ronon Dex, has that caused any problems? It must be quite intense for them, working on the same team?'

'From my own experience, they have proven on several occasions that their relationship, in no way, comes before the safety of their teammates or any other members of this expedition. If you're after a more detailed account, then I'm sure Colonel Sheppard would be happy to oblige.'

'Do you never modify the teams? Move people around?'

'I think trust is the best way to get a team to work well together.'

Woolsey gave her a rather condescending smile and returned to his clipboard, writing for several minutes before he looked up at her again.

'How do organise vacations for members of the expedition?'

'Every three Sundays, barring exceptional circumstances, we have a vacation day for all members of the expedition. And beyond that, we have a system in place where people can submit applications for more days and I will review them on an individual basis.'

'So, if-'

'Doctor Weir to the infirmary please.' Carson voice requested.

Elizabeth stood up and said, 'Could you excuse me? I think Colonel Sheppard is out of surgery.'

'Sit down Doctor Weir.'

'Excuse me?'

'We haven't finished here.'

'Colonel Sheppard has just come through major surgery, I need to go and access the situation.' She said urgently.

'Surely, you could radio Carson.'

'This isn't the sort of thing that you want to discuss when anybody could be listening in.'

Woolsey shrugged, 'Everybody knows that Colonel Sheppard was undergoing surgery today.'

'I don't have time for this.'

Elizabeth made a move towards the door, but was stopped in her tracks by Woolsey saying, 'If you choose to leave this interview Doctor Weir, I will be forced to come to the conclusion that the relationship between you and Colonel Sheppard is consequently impeding your judgement as leader of the expedition. Think very carefully before you leave Doctor Weir.'

Elizabeth gave him a look of defiance and left.

As she arrived at the infirmary, she was hyperventilating – a result of her worry about John and the possibility that she may well just have thrown her job in. She looked up at the ceiling and silently prayed, _please let him be better. _If John was better, then it was going to be worth it.

On seeing Carson's face she knew. That look of exhaustion, but underneath there was relief and pride. And at last she could breathe normally.

'Hey. How does it feel being able to use two legs?' She asked as she entered John's room.

'Not sure yet. It's feeling pretty numb. Like a really bad dead leg.'

'That's better than nothing though, right?'

'Anything's better than nothing. I'm still a little bit in shock that it actually worked.'

'You think you're shocked? Wait until Rodney finds out.' She grinned.

'I'm putting that off until later. So, just six months of physio and I should have a clean bill of health.'

'I bet you'll be back in five.'

'Hopefully. So, how was your interview with Woolsey?'

Elizabeth's heart missed a beat and she looked at John nervously before smiling.

'It went well.'

'Good.'

'Umm, John, would it be okay if I came back later? There's something I need to do.'

'And there was me hoping you were going to don a nurse's uniform and tend to me for the rest of the day.' He pouted.

She laughed, 'Later, maybe.'

The door to Richard Woolsey's quarters opened and he looked slightly surprised to see Doctor Weir standing on the other side with an envelope.

'Doctor Weir?'

She passed him the letter, 'This is my letter of resignation, and my application for the translator's job.'

He looked down, slightly dumbfounded, 'You seriously think you'll be able to continue here, watching somebody else fulfil the role as leader.'

'It's sure as hell got to be better continuing as leader without the support of the man I love.'

A/N: For those Woolsey fans (me being one of them), I'm very sorry to have written him as such a horrible character, but I literally didn't know any other IOA officials.


	14. Chapter 14

The morning after she resigned, Elizabeth Weir was sat on John Sheppard's bed in the infirmary playing solitaire with him. Nothing in her body-language hinted at the inner turmoil she was suffering; she was just happy to spend some time with John without worrying what people would think. Except they couldn't get too close because she hadn't told him yet.

She had intended to tell him last night, but he was already on the verge of sleep so she'd said good night and told him to rest. At that point she had resolved to tell him in the morning, but as she had walked to the infirmary she was so inundated with people asking if the email circulating about her resignation was true, that her confidence had slowly diminished and when she realised that he hadn't been informed yet, she had decided to put if off for a little longer and just enjoy his company.

He was going to seriously pissed off at her when she did. The whole point in them splitting up had been so they could continue to do the jobs they loved so much; he would hate the thought that she had given that up for him.

'Have you not got work to do or something?'

'I'm nursing you.' She teased.

'I meant proper work.' He said.

'It's all in Caldwell's capable hands, I'm sure.' Well, that wasn't technically a lie.

'If you say so.'

'I do.'

John shrugged and from outside they heard something fall to the ground and raised voices. They exchanged a curious glance, which was answered as Rodney and Ben marched into the side ward staring furiously at Elizabeth. Oh crap, she thought to herself.

'Have you gone insane?' Rodney demanded.

At this she rolled her eyes.

'Nothing's happening here. We're just playing solitaire.' John said, showing them the tablet.

'I don't mean you two and your game of 'solitaire'.' Rodney said using air quotations.

'What's going on?' John asked.

'Elizabeth's resigned.' Ben said.

John's head spun to look at her, 'Are you serious?'

'Yes.' She said in a small voice.

'Why didn't you tell me?' He asked, looking hurt.

'Because I knew how you'd react.'

'Why have you resigned? The letter just said 'personal reasons'.' Rodney asked, sounding perplexed.

'Are you really that obtuse?' Ben asked.

'What?' Rodney asked defensively.

'She's resigned because of him.' Ben nodded in John's direction.

'Hey.' John said, 'I had nothing to do with this.'

'Of course not.' Ben muttered cynically.

John sat up, 'You care to say that again because I will-'

'Stop it!' Elizabeth shouted.

The three men looked at her slightly sheepishly.

'This was _my _decision. John, I should have told you first, but I knew you would try and talk me out of it. I just can't do it anymore – I thought this city was enough, turns out that without you, it all feels a little bit superficial and empty.'

'I thought you two was just..._sex_.' Rodney said.

'For goodness sake.' Ben muttered.

Elizabeth gave him a reprimanding look, 'That was our cover story for the IOA.'

'Why didn't you tell me?' I'm your friend.' Rodney said to John.

'No disrespect, but you're not exactly brilliant at keeping things to yourself.'

'Still...' Rodney said.

'And how exactly is this going to work anyway? You living in America, him in Atlantis.' Ben asked.

'I've applied for a job here – the one we discussed.'

'You seriously think the IOA are going to be willing to forgive and forget and let you continue working here?'

'Maybe.' Elizabeth said doubtfully.

'What job?' John asked.

'Translating the Ancient data that Ben has discovered.'

'Oh come one,' Rodney said, 'You are totally over-qualified.'

'I'm hoping that might work in my favour.'

'You love...loved your job.' John said.

'But I love you more.'

He gently pulled her in for a kiss.

'Well, this day just keeps getting better and better.' Rodney said, in disgust.

They pulled away with and smiled at each other.

'Who's you replacement?' Ben asked.

'I didn't stop around to ask. I suspect it will be Colonel Caldwell.' Elizabeth said.

'Caldwell?' Rodney spat, 'I've been here for two and a half years! I know this place inside out.'

'I don't know for sure.' Elizabeth said.

'Let's be realistic here – he's earned a fair few brownie points with IOA with all the stuff he's informed them about out of 'duty'.' John pointed out.

'I still think you're mad.' Ben said, shaking his head.

'Sorry for disappointing you.' Elizabeth grinned.

Rodney and Ben looked at one another and left the room, looking incredibly downbeat. They didn't understand. And she'd always thought Ben would support her through this – he knew how much losing John had hurt her. In a way, it made her incredibly proud of her leadership of Atlantis. Every single person she had come across seemed genuinely upset that they wouldn't be working for her anymore, and she felt the same way about not being their leader anymore. Even through the bad times, she'd loved every second of it. It was going to be hard to let go, she thought wistfully.

'I don't want to work for Caldwell.' Rodney whined.

'Nope. Me neither. So you either suck it up or we're gonna need a plan.' Ben said.

'A plan? Don't you get it? There's nothing we can do – she wants this.'

'Oh I get it alright; she's been given an ultimatum. We just need to take the ultimatum out of the equation. You're a physicist; you should be good at that sort of thing.'


	15. Chapter 15

Elizabeth walked across the city to her meeting with Richard Woolsey which she suspected was going to be along the lines of, 'clear your quarters – you're going back to earth'. She had always know she was taking a massive risk in resigning – especially in the manner she had done it; revealing her feelings for John in the process.

After Ben and Rodney had left her had really rounded on, questioning the mindset she had been in when she had done it. Honesty was the best policy, and she laid down all her feelings over the past six months in attempt to show him that she knew what she was doing and that she had done the right thing. For her and for them. He hadn't bought that she had given it up all so easily, and, if she was honest, a few doubts and regrets were starting to creep. Being the leader of Atlantis, she had found, was the best experience of her life, and it was quite disconcerting to accept that it was all over. And she was probably going home.

Her attempts to talk to Ben had gone awry as well. The whole time she had been there, explaining why she had done what she had, he had continued to type away at his laptop, occasionally grunting to show he was listening. And as soon as Rodney had turned up with a file, she had been ushered out. Since when had those two been such great mates anyway?

Steven Caldwell had taken over the leadership of the city, much to the displeasure of many. She had dropped by his quarters to congratulate him, and wasn't entirely sure what to think. He seemed both smug and irritated in equal measures.

For the first time in two days, she walked into her...Caldwell's office and sat down to wait for Richard Woolsey. After a few minutes she heard heavy footsteps marching into the office and a pile of papers were thrust into her hand by an irate looking Woolsey who then proceeded to pace around the office. Confused, she looked down at the first paper which read 'Notification of Resignation' signed by Rodney McKay.

'I don't understand.' She said.

'Look at them. Look at them all.' He barked.

Again she looked down at the pile and began flicking through the sheets. Each said the same thing with one exception, they were all signed by different members of the expedition.

'There are one hundred and sixty two letters there, out of one hundred and sixty five people who work here in Atlantis. Do you have any idea what you have done? I don't appreciate being held to ransom Doctor Weir.' Woolsey said through gritted teeth.

'It's not pleasant, is it?' She asked cooly.

Woolsey gave her an irritated look.

'Do you really think I'm behind this?' She asked.

'You and your accomplices.'

'My accomplices?'

Woolsey handed her another two piles of papers, the first of which she began to read and immediately she recognised it. It was the book documenting all her achievements as the leader of Atlantis which Rodney had wrote when undergoing a heightened sense of intelligence after being hit by the Ancient machine which had been used to speed up ascending.

'I haven't had time to read it all, but the main point Doctor McKay seems to be making is that you have the united this expedition and, without you, Atlantis would have been destroyed. I don't know how he's found the time to write it five hundred pages in the last two days.'

Elizabeth raised an eyebrow, but didn't enlighten him.

'And the second is by Doctor Ben Hill, documenting a series of decisions you have made during and after you relationship which prove that your judgement hasn't been impaired by your feelings for Colonel Sheppard.'

'Richard I didn't know anything about this.' Elizabeth said honestly, 'I'm sure that everybody can be persuaded to change their minds.'

'The message is clear Doctor Weir. In this city we have a collection of the most skilled and intelligent people, and the only person they want to work for is you.'

Woolsey sat down and sighed before looking at her. A small feeling of hope was beginning to surface in Elizabeth.

'I don't know what to do. I'm out of my depth. I didn't even want to conduct this review.' Woolsey said wistfully.

'You should do what you think is best for the city.'

'I'm not sure my colleagues will share the same opinion though.' He said with a small smile.

'Perhaps with some gentle persuasion... You are in charge of this review, and ultimately, it's your call.' Elizabeth suggested, pushing Ben's document forward.

'Colonel Caldwell isn't going to be happy.' Woolsey said, eying the document.

'I doubt he'd be happy leading an empty city either.'

Woolsey stared at her for what must have been minutes. In all that time her eyes never wavered from his and finally he stood up and held out his hand.

'I think we can forget about all of the resignation letters over the past two day, Doctor Weir. I'm sure they,' he nodded towards the control room, 'won't mind when they hear that you have been reinstated as the leader of Atlantis.'

Elizabeth stood up and accepted his hand.

'Are you sure?'

'I think so. I'm counting on the fact that I can get the Presidents support. He's always had a soft spot for you. It's not going to be an easy ride though; you'll be under even more scrutiny.' He warned.

'I'll cope. Do you want me to inform Colonel Caldwell?'

'No, it might sound better coming from me.'

'There are a few people I'd like to see, is it okay if I leave?'

'Certainly. Good luck Doctor Weir.'

'Thank you very much Richard.'

With a final smile at her he began to collect the resignation papers from the desk and she left, barely able to keep the grin off her face. Her first instinct was to go and see John, but there were two people who she owed everything to and she was going to thank them first. She found them bickering in Ben's lab and stood and observed them for almost two minutes before they noticed her. When they realised she was there, they exchanged a nervous glance.

'That little stunt of yours, a little risky wasn't it?'

'That depends on if it worked.' Ben said.

'Woolsey is going to ignore the resignation letters.'

Ben's shoulders visibly dropped in dismay, and a looked of disappointed disbelief came over Rodney's face.

'Including mine.'

'That's fantastic!' Ben said, hugging her.

'See, told you it would work.' Rodney said to Ben.

'So whose idea was this?'

'Mine.' Rodney said smugly.

'Ours.' Ben said.

'Well, I came up with my book and the list of decisions, Ben came up with persuading everyone to resign.' Rodney said.

'Which was the most persuasive argument.' Ben said.

'No it wasn't! Without my-'

'Anyway,' Elizabeth cut in, 'I'm going to go and tell John. I just wanted to say thank you.'

'Anytime.'

'You're welcome.'

As Elizabeth reached the door, she turned back and said, 'You two should work together more often. You make a good team.'

With that, she left and headed to the infirmary, practically skipping – partly through joy and partly through the urge to get to John immediately. They could be together, doing the jobs they loved. It was like a dream. Admittedly it was a dream where they could be attacked or killed at any moment, but she had a feeling it was all going to be worth it.

'So, is he sending you back to earth? John asked as soon as she entered the ward.

Instead of answering immediately, she went over to him and kissed him passionately.

'I'll take that as a no then. He's letting you stay on as the translator?'

'He's gone one better, actually. He's reinstated me as leader.'

John mouth fell open, 'What? How?'

'Rodney and Ben came up with a little plan. I'll fill you in later. For now, I'd like to spend some time with my boyfriend.' She said leaning out to kiss him again.

'Woolsey's cool with this?' John asked, pulling away.

'Yes. Well, as cool as Woolsey can get.' Elizabeth grinned.

'I'm not still medicated up, right?'

'This is one hundred per cent real.'

This time, he relented and let her kiss him.

**The End**

A/N: I hope you all enjoyed it, and it wasn't too implausible. Thank you all so much for the supportive reviews.


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